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From Tom Devel <deve...@gmail.com>
Subject Re: Is it necessary to put UMLS login into files when passing them with -D to the JVM?
Date Fri, 06 Mar 2015 20:42:40 GMT
Sean,

On Fri, Mar 6, 2015 at 2:30 PM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:

> Hi Tom,
>
> > I am passing my UMLS login and password on startup as arguments ...
> "-Dctakes.umlsuser=myusername -Dctakes.umlspw=mypassword"
> That is fine.  If I understand correctly you are already running this way
> without problem.  The comments in the .xml files should probably be
> extended to include mention of the cmd parameters.
>
>
Yes, I am getting validation output as follows: INFO UmlsUserApprover -
UMLS Account at https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user
xxxxxxx has been validated


> > [I] downloaded [AggregatePlaintextFastUmlsProcessor.xml] from the svn
> and replaced the old cTAKES 3.2.1 ...
> I think that this should be fine.  Java code for each annotator may have
> changed, but I don't think that any class names (by which annotators are
> called) have changed.  The best way to know for certain is to run it, and
> if you haven't seen any problems then I think that you are in good shape.
>
>
It <seems> to work without showing any exceptions so far.

Thanks,
Tom

Sean
>
> -----Original Message-----
> From: Tom Devel [mailto:develxy@gmail.com]
> Sent: Friday, March 06, 2015 3:20 PM
> To: dev@ctakes.apache.org
> Subject: Is it necessary to put UMLS login into files when passing them
> with -D to the JVM?
>
> Hi,
>
> in AggregatePlaintextFastUMLSProcessor.xml of cTAKES it states that:
>
> [...] Please update DictionaryLookupAnnotatorUMLS.xml file with your UMLS
> username and password.
>
> Similarly, in AggregatePlaintextFastUMLSProcessor.xml from
> https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D344&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ZOef73O4fpDF9CZPAZHmVyDZDQDa6jKWyTTU1kikj9o&s=7C1osQzBp5-aSIXPeqWPXcafrLDGCeEkR3sfbiJMRDQ&e=
>
> [...] Please update
> resources/org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml file
> with your UMLS username and password
>
> I am passing my UMLS login and password on startup as arguments, when
> starting the either CVD/CPE or org.apache.uima.examples.cpe.SimpleRunCPE
> argumets such as:
>
> "-Dctakes.umlsuser=myusername -Dctakes.umlspw=mypassword"
>
> In such a case, it is still necessary to modify the file(s) above?
>
> Additional question: It seems that the
> AggregatePlaintextFastUMLSProcessor.xml from
> https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D344&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ZOef73O4fpDF9CZPAZHmVyDZDQDa6jKWyTTU1kikj9o&s=7C1osQzBp5-aSIXPeqWPXcafrLDGCeEkR3sfbiJMRDQ&e=
> has some nice improvements (using DrugNER and default fast pipeline). I
> just downloaded it from the svn and replaced the old cTAKES 3.2.1 file with
> this one, and it seems to run just fine and cTAKES does annotations. Can
> somebody from the devs or users tell me if this manual replacement step is
> OK and does not break anything that I am not aware of?
>
> Many thanks for answers on any of my questions, Tom
>

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